As revealed by Sportsmail, Hughes allowed a contract deadline to pass without taking up the option of a further year with the west London club.
However, the former Manchester City boss insisted his decision was based solely on what he believed he could achieve at Fulham. He was at pains to point out he had not been in contact with Aston Villa or Chelsea, the two clubs he has been linked with.
Gone: Mark Hughes feels he has taken Fulham as far as he can
Hughes delayed his initial decision on Wednesday night following talks with Fulham chief executive Alistair Mackintosh, who asked him to reconsider and who is believed to have offered the 47-year-old a two-year contract.
Hughes said: 'I hope the supporters and all those connected with the club will understand I wish to move on to further my experiences.
On the up: Fulham had an impressive season, eventually finishing eighth
'I would also like to take this opportunity to clarify that neither myself nor my representative have approached or been approached by another club. This decision to leave Fulham has not been influenced by any outside party.'
Fulham will need to find a replacement quickly as the club play in the qualifying round of the Europa League on June 30.
No return: Gerard Houllier has left Aston Villa following his heart scare
Villa chief executive Paul Faulkner has assured Mackintosh that no contact has been made with Hughes's agentfollowing Gerard Houllier's departure but the odds on the Welshman managing the Midlands club were cut dramatically last night.
Coincidentally, given that Hughes remains among the favourites to succeed Houllier at Villa Park, former Villa boss Martin O'Neill could be a prime candidate to replace him at Craven Cottage.
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Source: Daily Mail
Source: Daily Mail